Search

Synthesis of graphene with reduced use of chemical reagents is essential for manufacturing scale-up and to control its structure and properties. In this paper, we report the mechanism for exfoliating graphene from graphite slabs using laser impulse. We set up a molecular dynamics model that accounts for the charge-mediated inter-atomic potential along with the forces from electromagnetic fields of a laser pulse. The role of different laser fluences on the exfoliation process of graphene quantified in terms of the interlayer energy transition, inter-layer displacement jump, and thermal shock propagation in graphene-graphite system. The simulation results confirm the exfoliation of a single layer graphene sheet for the laser power ranging from 100 × 10 − 14 to 2000 × 10 − 14 J/nm2. With an increase of laser fluence from 2000 × 10 − 14 to 4000 × 10 − 14 J/nm2, there is an increase in the graphene yield via the layer-after-layer exfoliation. The bridging bond dynamics between the successive graphene layers govern the exfoliation of the second layer. The results indicate promises for producing chemical-free graphene on a large scale for industrial applications. [ABSTRACT FROM AUTHOR]

The ability to automatically extend and improve molecular force fields to accurately describe an ever wider range of compounds is a key enabler for the application of molecular modelling of chemicals and materials in industry. In this work we have developed a set of tools to process structural data available in well-known databases, to find deficiencies in the force field, and where necessary, automatically fit force- field parameters to on-the-fly calculated quantum data based on Density Functional Theory, supplemented by experimental data. The protocols have been applied to structures from the Maybridge, PoLyInfo and ILThermo databases, covering drug-like molecules, polymers and ionic liquids respectively. We demonstrate that the new version of the force field can type all structures in the extended data set without missing parameters, with a similar high-quality prediction of geometry (bonds, angles, torsions), energy and forces of earlier versions. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations are more frequently being utilised to predict macroscale mechanical properties as a result of atomistic defects. However, the interatomic force field can significantly affect the resulting mechanical properties. While several studies exist which demonstrate the ability of various force fields to predict mechanical properties, the investigation into which is most accurate for the investigation of vacancies is limited. To obtain meaningful predictions of mechanical properties, a clear understanding of force field parameterisation is required. As such, the current study evaluates various many-body force fields to demonstrate the reduction in mechanical properties of iron and iron–chromium due to the presence of vacancies while undergoing room temperature atomistic uniaxial tension. Reduction was normalised in each case with the zero-vacancy elastic modulus, removing the need to predict an accurate nominal elastic modulus. Comparisons were made to experimental data and an empirical model from literature. It was demonstrated that accurate fitting to vacancy formation and migration energy allowed for accurate predictions. In addition, bond-order based force fields showed enhanced predictions regardless of fitting procedure. Overall, these findings highlight the need to understand capabilities and limitations of available force fields, as well as the need for enhanced parameterisation of force fields. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations, which take place on the atomistic scale, are now being used to predict the influence of atomistic processes on macro-scale mechanical properties. However, there is a lack of clear understanding on which potential should be used when attempting to obtain these properties. Moreover, many MD studies that do test mechanical properties do not actually simulate the macro-scale laboratory tension tests used to obtain them. As such, the purpose of the current study was to evaluate the various types of potentials for their accuracy in predicting the mechanical properties of iron from an atomistic uniaxial tension test at room temperature. Results demonstrated that while EAM and MEAM potentials all under predicted the elastic modulus at room temperature, the Tersoff and ReaxFF potentials were significantly more accurate. Unlike EAM and MEAM, both the Tersoff and ReaxFF potentials are bond order based. Therefore, these results demonstrate the importance of considering bonding between atoms when modelling tensile tests. In addition, the ReaxFF potential also accurately predicted the Poisson's ratio, allowing for complete characterisation of the material's behaviour. Overall, these findings highlight the need to understand the capabilities and limitations of each potential before application to a problem outside of the initial intended use. [ABSTRACT FROM AUTHOR]

The optimisation of a peptide-capped glycine using the novel force field FFLUX is presented. FFLUX is a force field based on the machine-learning method kriging and the topological energy partitioning method called Interacting Quantum Atoms. FFLUX has a completely different architecture to that of traditional force fields, avoiding (harmonic) potentials for bonded, valence and torsion angles. In this study, FFLUX performs an optimisation on a glycine molecule and successfully recovers the target density-functional-theory energy with an error of 0.89 ± 0.03 kJ mol−1. It also recovers the structure of the global minimum with a root-mean-squared deviation of 0.05 Å (excluding hydrogen atoms). We also show that the geometry of the intra-molecular hydrogen bond in glycine is recovered accurately. [ABSTRACT FROM AUTHOR]

By combining the bottom-up and top-down approaches, we have developed a new all-atom (AA) force field from quantum mechanics and experimental data and a new coarse grained (CG) force field from AA simulation and experimental data, for polydimethylsiloxane (PDMS). The AA force field is developed based on the TEAM force field database. The CG force field uses a mapping rule that splits the connecting oxygen into neighbouring CG beads to maintain the charge neutrality of the beads, analytical functional forms including anharmonic terms in the valence terms, and the temperature-dependent free-energy functional form to describe the inter-bead interactions. Broad range of thermodynamic properties of PDMS including density, surface tension, solubility parameter, radius of gyration and glass transition temperature are calculated to validate the force fields, and good agreements with the experimental data are obtained. [ABSTRACT FROM PUBLISHER]

The paper deals with the methodology of film growth simulations using classical molecular dynamics and an empirical interaction potential. We focus on the effect of the cut-off distance (rC) of the short-range part of the potential. On the one hand, we find thatrCdoes not affect the qualitative conclusions of the simulations and that its quantitative effect is in the logical direction (better crystallinity at higherrC). On the other hand, we show that the aforementioned quantitative effect is very strong, and clearly underestimated in the literature. The film crystallinity is affected by (non-)neglecting of as seemingly low energies as several meV per bond. The results are important for the design of growth simulations of crystalline films and for the correct interpretation of their results. [ABSTRACT FROM AUTHOR]

Aqueous ethanol mixtures are studied through molecular dynamics simulations with the focus on exploring how various force field models reproduce the association and its influence on selected thermo-physical properties of these mixtures. The most important conclusion seems to be the inadequacy of all classical force fields to reproduce the very peculiar shape of the excess enthalpy of these mixtures, as a function of the ethanol concentration, neither quantitatively nor qualitatively. The Kirkwood–Buff (KB) integrals calculated using the simulation data follow the same trends as the experimental ones. This suggests complicated correlation of the excess enthalpy with the concentration fluctuation and clustering in these mixtures. The KB force field shows better overall agreement with experimental results than the other studied models. [ABSTRACT FROM PUBLISHER]

One of the challenges in the area of molecular simulation of biointerfaces is to ensure that the interatomic potentials used to describe such interfaces capture the essential chemistry and physics of the system. Here, we report the conformational testing of the inter-operability of the CHARMM and SPC/Fw force fields, the compatibility of which is essential for successful incorporation of a description of biomolecules into current biomineralisation force fields. The effect of the new water model, SPC/Fw, on the conformational equilibrium of two contrasting exemplar tripeptide sequences, RGD and SPT, as described by the CHARMM force field, has been probed by the analysis of results generated from replica-exchange molecular dynamics simulations. We compare the ensemble of conformational states generated from the CHARMM-SPC/Fw force fields with those obtained from the more typical CHARMM-TIPS3P combination. Analysis shows that the findings from the two force field combinations compare very favourably for equilibrium structure determination for both peptides. [ABSTRACT FROM AUTHOR]

We present a transferable force field able to model the structure of zeolites when different cation types are considered. Based on simple functional forms and interactions, it can be easily implemented in most common molecular simulation codes. The optimised force field is validated on structural properties (lattice parameters and Si–O–Al angles) for a large variety of zeolites, including faujasites of different Si/Al ratio and different extra-framework cation types (Li+, Na+, K+, Mg2+, Ca2+and Co2+). The transferability of the force field was successfully tested on zeolites of different topologies such as FAU, LTA, MFI, FER and TON. The predictive capabilities of the potential were tested on structural deformations of alkaline earth Na, Co-X faujasites with different ion-exchange ratios. [ABSTRACT FROM PUBLISHER]

Secondary structures of antimicrobial peptides (AMPs) play an important role in their activity. The AMP cecropin P1, like most other anti-microbial peptides, is known to form a helix at the interface of bacterial cell membranes. This structure is fundamental to its activity and its ability to destroy the membrane. In contrast, as reported in experimental measurements, this peptide unfolds in bulk water. We analysed this behaviour using two different force fields, CHARMM22/CMAP and AMBER ff99SB. Although these two force fields are commonly used in molecular dynamics (MD) and have been extensively validated, we observed two sharply different results. A sodium dodecyl sulphate (SDS) micelle was used to model the bacterial membrane using MD simulations. CHARMM22 resulted in a peptide that stays mostly folded in both environments (bulk water and SDS), while AMBER correctly predicted the unfolding in bulk water and produced results that closely match the available experimental data. We further computed the free energy of folding and unfolding, using the adaptive biasing force method, to get a complete picture of the energy barriers and the different metastable states. To get further insights into the interaction of the peptide with its environment, we computed the average number of hydrogen bonds between different components versus the folding reaction coordinate. [ABSTRACT FROM PUBLISHER]

Force fields for engineering applications are often parameterised using strategies based on quantum mechanicalab initiocalculations and thermodynamic properties from experiment. An automated procedure for adjusting molecular model parameters to experimental thermodynamic property data is introduced. The process accelerates the development of molecular models by an efficient use of parallel computing power and an autonomous progress of the model development without any user interaction. As a case study, the procedure is applied to the parameterisation of a molecular model for acetonitrile. The resulting model reproduces vapour–liquid equilibrium data of acetonitrile with an accuracy of 0.1% for the saturated liquid density, 4.9% for the vapour pressure and 3.7% for the enthalpy of vaporisation. These accuracies are superior to data obtained with previously published force fields for acetonitrile. [ABSTRACT FROM AUTHOR]

We have previously proposed a force-field refinement method. This method consists of minimising the sum of the square of the force acting on each atom in the proteins with the structures from the Protein Data Bank. In addition, we also proposed a new backbone-torsion-energy term, which is represented by a double Fourier series in two variables, the backbone dihedral anglesand. In this paper, we apply our optimisation method and backbone-torsion-energy term to AMBER ff94 (ff96) force field for molecular simulation of protein systems. The results imply that the new force-field parameters give structures of two peptides more consistent with the experimental implications for secondary-structure-forming tendencies than the original force field. [ABSTRACT FROM AUTHOR]

Computer simulation of biomolecular systems has become a standard research instrument for the investigation of biomolecular processes at the atomic level of modelling and interpretation. A bird's eye view of the development of simulation methodology, of biomolecular interaction functions and simulation software is presented, together with the challenges in regard to these three aspects of biomolecular simulation. [ABSTRACT FROM AUTHOR]

We have carried out a structural and vibrational study for 5-phenyl-1,3,4-oxadiazole-2-thiol by using the infrared (IR) spectrum and theoretical calculations. For a complete assignment of the compound IR spectrum, density functional theory calculations were combined with Pulay's scaled quantum mechanical force field methodology in order to fit the theoretical wavenumber values to the experimental ones. An agreement between theoretical and available experimental results was found. The theoretical vibrational calculations allowed us to obtain a set of scaled force constants fitting the observed wavenumbers. The results were then used to predict the Raman spectra, for which there are no experimental data. The nature of the benzyl and oxadiazole rings was studied by means of natural bond order and atoms in molecules theory calculations. In addition, the frontier molecular (highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO)) orbitals were analysed and compared with those calculated for the oxadiazole molecule. [ABSTRACT FROM PUBLISHER]

An improved torsional force field for cis-enol malonaldehyde is presented. First, the conformational potential energy has been calculated by ab initio method at MP2/6-31G** level as a function of two torsional angles around C–C and C–O single bonds. Then, the calculated 2D potential energy surface has been fitted to a potential function, where cross terms of the two dihedrals are added to the ordinary single cosine terms of the optimised potentials for liquid simulations all atom (OPLS-aa) type. The optimised function excellently reproduces the energies with the standard deviation as small as 1.9 kJ/mol. The function may be used easily in the molecular dynamics calculation. [ABSTRACT FROM PUBLISHER]

A united-atom potential model for naproxen suitable for molecular dynamics (MD) simulation has been developed. The charge distribution is approximated by point charges obtained from ab initio calculations using the CHELPG method. Also the intramolecular interactions such as bond and angle vibration, and the torsion potential are obtained from ab initio calculations. The dispersive interaction contribution is taken from the literature. By MD simulation using a naproxen film in slap geometry, the temperature dependence of the density, surface tension and self-diffusion coefficient as well as the melting temperature for the developed potential model are obtained. [ABSTRACT FROM PUBLISHER]

This paper is part of our pursuit to develop an efficient procedure for optimising parameters that provide a reliable foundation for highly predictive molecular simulations. We tested whether DesParO, a mathematical tool originally used in automotive design, is suitable for creating Lennard-Jones (LJ) parameters that accurately reproduce the experimental phase behaviour for our test compound ethylene oxide (EO). So, we created a multitude of diverse random parameter sets, performed Gibbs ensemble Monte Carlo simulations and collected the resulting physical properties. On that data basis, DesParO derived a meta-model through a multidimensional interpolation. We then explored, in an interactive fashion unique to DesParO, the LJ parameter space and selected some suitable parameter sets, which were then tested by simulations. For EO, the selected parameter sets were indeed superior to the initial parameters. Furthermore, the new parameters can be reliably used as input for further optimisation by other methods, resulting in extremely robust LJ parameters. Beyond the prediction of parameter sets, DesParO enabled us to examine the underlying parameter-property relationships that help us solve future optimisation problems by creating subordinate parameter optimisation tasks in a systematic manner; this ability makes DesParO a valuable tool in the overall optimisation process. [ABSTRACT FROM AUTHOR]

We have previously proposed a method for refining force-field parameters of protein systems, which consists of minimising the summation of the square of the force acting on each atom in the proteins with the structures from the protein data bank (PDB). The results showed that the modified force-field parameters for all-atom model gave structures more consistent with the experimental implications than the original force fields. In this work, we applied this method and a new method to the OPLS-UA force field. In the new method, we perform a minimisation of the average of the root-mean-square deviation of various protein structures from the native structure. We selected some torsion-energy parameters for this optimisation, and 100 molecules from the PDB were used. The results imply that the new force-field parameters gave structures of two peptides more consistent with the experimental implications for the secondary structure-forming tendencies than the original OPLS-UA force field. [ABSTRACT FROM AUTHOR]

While force-field development has been discussed extensively in the literature, the question of what analytical expressions make the best function choices, particularly in the context of matching quantum mechanic potential energy surfaces (PES), is less explored. Traditional forms based upon harmonic oscillators and Lennard-Jones types have dominated the field owing to the focus on fitting properties. However, with the advent of gradient-fitting approaches, it is now possible with the correct force-field expressions to achieve consistent high-accuracy results with molecular dynamics calculations. Using the general principle that power series can fit surfaces of any shape well, we have utilised harmonic series functions to fit a two-body PES represented by a Morse function. The harmonic functions are fast because they have only integer exponents, and they fit accurately with a limited number of terms. [ABSTRACT FROM AUTHOR]

We performed folding simulations of three proteins using four force fields, AMBER parm96, AMBER parm99, CHARMM 27 and OPLS-AA/L, in order to examine the features of these force fields. We studied three proteins, protein A (all α-helix), cold-shock protein (all β-strand) and protein G (α/β-structures), for the folding simulations. For the simulation, we used the simulated annealing molecular dynamics method, which was performed 50 times for each protein using the four force fields. The results showed that the secondary-structure-forming tendencies are largely different among the four force fields. AMBER parm96 favours β-bridge structures and extended β-strand structures, and AMBER parm99 favours α-helix structures and 310-helix structures. CHARMM 27 slightly favours α-helix structures, and there are also π-helix and β-bridge structures. OPLS-AA/L favours α-helix structures and 310-helix structures. [ABSTRACT FROM AUTHOR]

We propose a new method of optimisation of backbone torsion-energy parameters in the force field for molecular simulations of protein systems. This method is based on the idea of balancing the secondary-structure-forming tendencies, namely, those of α-helix and β-sheet structures. We perform a minimisation of the backbone dihedral angle-based root-mean-square deviation of the helix and β structure regions in many protein structures. As an example, we optimised the backbone torsion-energy parameters of AMBER parm96 force field using 100 protein molecules from the Protein Data Bank. We then performed folding simulations of α-helical and β-hairpin peptides, using the optimised force field. The results imply that the new force-field parameters give structures more consistent with the experimental implications than the original AMBER parm96 force field. [ABSTRACT FROM AUTHOR]

We examined a new backbone torsion-energy term proposed by us in the force field for protein systems. This torsion-energy term is represented by a double Fourier series in two variables, namely the backbone dihedral angles φ and ψ. It gives a natural representation of the torsion energy in the Ramachandran space in the sense that any two-dimensional energy surface periodic in both φ and ψ can be expanded by the double Fourier series. We can then easily control secondary-structure-forming tendencies by modifying the torsion-energy surface. For instance, we can increase or decrease the α-helix-forming-tendencies by lowering or raising the torsion-energy surface in the α-helix region and likewise increase or decrease the β-sheet-forming tendencies by lowering or raising the surface in the β-sheet region in the Ramachandran space. We applied this torsion-energy modification method to six force fields, AMBER parm94, AMBER parm96, AMBER parm99, CHARMM27, OPLS-AA and OPLS-AA/L, and demonstrated that our modifications of the torsion-energy terms resulted in the expected changes of secondary-structure-forming tendencies by performing folding simulations of α-helical and β-hairpin peptides. [ABSTRACT FROM AUTHOR]

Compared with imidazolium-based ionic liquids (ILs), phosphonium-based ILs have been proven to be more stable in thermodynamics and less expensive to manufacture. In this work, a kind of phosphonium-based IL, [PC6C6C6C14][Tf2N], was studied under several conditions using molecular dynamics simulations based on both the all-atom force field (AAFF) and the united-atom force field. Liquid density was calculated to validate the force field. Compared with experimental data, good agreement was obtained for the simulated density based on the AAFF. Heat capacities at constant pressure were calculated at several temperatures, and good linear relationships were observed. Self-diffusion coefficients, viscosities and conductivities were also calculated to study the dynamics properties of this IL. The viscosity of this IL at 293 K was also compared with experimental data, and the error was in a reasonable range. In order to depict the microstructures of the IL, centre-of-mass and site-to-site radial distribution functions were employed. In addition, spatial distribution functions were investigated to present the more intuitive features. [ABSTRACT FROM AUTHOR]

Controlling surface wettability, expressed in terms of contact angle, is a significant issue in nanotechnology. In this paper, through extensive molecular dynamics simulations, we show that the contact angle of water droplet on a TiO2 surface is considerably influenced by the temperature variations, i.e. as the temperature increases, the contact angle decreases and the surface becomes more hydrophilic. We address the issue of accurate force fields and determine the partial charges that can closely reproduce the experimental contact angle. Detailed understanding of the temperature-dependent variation of contact angle is developed by hydrogen bonding analysis. [ABSTRACT FROM AUTHOR]

The effect of partial charge parameterization on the fluid phase behavior of dimethyl ether (DME) is investigated with grand canonical Monte Carlo simulations coupled with histogram reweighting techniques. A total of 16 optimized parameter sets are presented, covering a range of dipole moments from 0 to 2.4 D. Although all 16 parameter sets are able to reproduce experimental saturated liquid densities, only six of the parameter sets, corresponding to - 0.433 ≤ qO ≤ - 0.58 are able to simultaneously produce accurate predictions for the saturated liquid densities and vapor pressures over the temperature range 280 ≤ T ≤ 380. The heat of vaporization, acentric factor and radial distributions are also presented. [ABSTRACT FROM AUTHOR]

1,4-dioxane, a cyclic ether, is an emerging contaminant which is difficult to remove from water with conventional water treatment methods and resistant to biodegradation. Once a reliable force field is developed for 1,4-dioxane, molecular simulation techniques can be useful to study alternative adsorbents for its removal. For this purpose, we carried out Monte Carlo simulations in a constant volume Gibbs Ensemble to generate a force field which is capable of predicting the vapour–liquid coexistence curve and critical data of 1,4-dioxane. Results are given in comparison with experimental data and results from simulations with other force fields. Liquid densities and critical temperature are predicted in excellent agreement with experimental data using the new force field. At high temperatures, predicted vapour densities are in good agreement with experimental data, however, at lower temperatures the predicted vapour densities deviate about an order of magnitude from the experimental values. The critical density is slightly underestimated with our new force field. However, overall, the results of simulations with the new parameters give much better agreement with experimental data compared to the results obtained using other force fields. [ABSTRACT FROM AUTHOR]

The direct reaction field (DRF) approach has proven to be a useful tool to investigate the influence of solvents on the quantum/classical behaviour of solute molecules. In this paper, we report the latest extension of this DRF approach, which consists of the gradient of the completely classical energy expressions of this otherwise QM/MM method. They can be used in (completely classical) molecular dynamics (MD) simulations and geometry optimizations, that can be followed by a number of single point QM/MM calculations on configurations obtained in these simulations/optimizations. We report all energy and gradient expressions, and results for a number of interesting (model) systems. They include geometry optimization of the benzene dimer as well as MD simulations of some solvents. The most stable configuration for the benzene dimer is shown to be the parallel-displaced form, which is slightly more stable (0.3 kcal/mol) than the T-shaped dimer. [ABSTRACT FROM AUTHOR]

In the absence of reliable experimental data, significant difficulties have been encountered in the design of force fields for the simulation of imidazolium-based ionic liquids. This review examines the problems encountered and improvements made in developing force fields for the study of imidazolium-based ionic liquids. The performance of these models is assessed with respect to the prediction of structural and dynamical properties and compared with results from recently published ab initio molecular dynamics studies. Many of the original force fields have now been employed to study interfacial, mixing and solvation phenomena and in association with the ab initio molecular dynamics results, these studies have highlighted a number of potential areas for improvement, particularly with respect to the accurate modelling of charge transfer effects and hydrogen bond formation. [ABSTRACT FROM AUTHOR]

Protein folding requires extensive changes of backbone and sidechain dihedral angles, whose energy barriers constitute obstacles for the folding kinetics. Folding of small proteins is furthermore thought to be path-independent. Here, we propose that time-consuming all-atom protein folding simulations may be accelerated through a reduction of the dihedral barriers of the force field. In order to investigate this hypothesis, we performed various folding simulations of two small proteins. We report an acceleration towards smaller root-mean-square deviations from the native protein structure using our proposed method. [ABSTRACT FROM AUTHOR]

The ability of five different force fields (MM2, MM3, AMBER, OPLS, MMFF) to calculate relative conformational energies of seven molecules is compared to results at the MP2/aug-cc-pVTZ level. It is found that the quality of the results deteriorates as the polarity of the molecules increases for all force fields, strongly indicating that the use of fixed partial charges for representing the electrostatic interaction limits the accuracy that can be obtained. [ABSTRACT FROM AUTHOR]